A new understanding of the damage formation mechanisms in Si is developed and investigated over an extended range of ion energy, dose, and irradiation temperature. A simple model for dealing with ion-induced damage is proposed, which is shown to be applicable over the range of implantation conditions. In particular the concept of defect "excesses" will be discussed. An excess exists in the lattice when there is a local surplus of one particular type of defect, such as an interstitial, over its complimentary defect (i.e., a vacancy). Mechanisms for producing such excesses by implantation will be discussed. The basis of this model specifies that accumulation of stable lattice damage during implantation depends upon the excess defects and not the total number of defects. The excess defect model is validated by fundamental damage studies involving ion implantation over a range of conditions. Confirmation of the model is provided by comparing damage profiles after implantation with computer simulation results. It will be shown that transport of ions in matter (TRIM) can be used effectively to model the ion-induced damage profile, i.e. excess defect distributions, by a simple subtraction process in which the spatially correlated defects are removed, thereby simulating recombination. Classic defect studies illuminate defect interactions from concomitant implantation of high- and medium-energy Si+-self ions. Also, the predictive quality of the excess defect model was tested by applying the model to develop several experiments to engineer excess defect concentrations to substantially change the nature and distribution of the defects. Not only are the excess defects shown to play a dominant role in defect-related processing issues, but their manipulation is demonstrated to be a powerful tool in tailoring the implantation process to achieve design goals. Pre-amorphization and dual implantation of different energetic ions are two primary investigative tools used in this work. Various analyses, including XTEM, RBS/channeling, PAS, and SIMS, provided experimental verification of the excess defect model disseminated within this dissertation.